9VV0 | pdb_00009vv0

CryoEM structure of EV-D68 strain Fermon in complex with MFSD6-L3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

A dual-receptor checkpoint primes enterovirus D68 for respiratory cell entry.

Liang, S.Guo, H.Xu, Z.Liu, Z.Yang, W.Liu, X.Wei, Z.Hou, J.Huang, W.Wang, W.Li, J.Ma, W.Deng, Z.Qian, H.Wang, Y.Liu, J.Rao, Z.Wei, W.Lou, Z.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-75856-2
  • Primary Citation Related Structures: 
    23AY, 23BG, 23BX, 23PS, 9VV0, 9W0D, 9W0E, 9W0I, 9W0J, 9W0K, 9W34, 9W4O, 9W4Y

  • PubMed Abstract: 

    MFSD6 is a newly identified receptor that mediates the invasion of respiratory cells by enterovirus D68 (EV-D68), a non-polio enterovirus that causes severe respiratory disease and poliomyelitis-like illness in children. Here, we report near-atomic-resolution cryo-electron microscopy (cryo-EM) structures of historical and contemporary AFM-associated EV-D68 strains, together with their complexes bound to the third extracellular loop of MFSD6 (MFSD6-L3). These structures uncover a previously unrecognized "binary gating switch" mechanism of virus-receptor engagement that differs from the reported model. In this mechanism, the N200-V208 segment of MFSD6, carrying a glycosylated Asn207, inserts into one capsomer, whereas the sialyl-Gal-terminated glycan of MFSD6 engages an adjacent capsomer. Neu5Ac binding induces conformational rearrangements that expel the pocket factor, destabilize the virion, and prime infection. Functional analyses further define the contributions of the receptor-contacting residues and glycans to viral attachment and entry. Together, our findings refine the molecular basis of EV-D68 recognition of MFSD6 and reveal a glycan-mediated dual-lock mechanism that may enhance receptor specificity, prevent premature uncoating, and ensure productive infection only upon engagement of the correct host receptor. These results provide broader insight into enterovirus tropism and establish a framework for structure-guided antiviral design.


  • Organizational Affiliation
    • Pathogen and Anti-Infection Technology Innovation Center, Yanzhao Advanced Biotechnology and Medicine Laboratory, Institute of Tsinghua University, Hebei, China.

Macromolecule Content 

  • Total Structure Weight: 111.21 kDa 
  • Atom Count: 6,553 
  • Modeled Residue Count: 829 
  • Deposited Residue Count: 993 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP1296enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
Entity Groups
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UniProt GroupQ68T42
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP2248enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
Entity Groups
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UniProt GroupQ68T42
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
P1247enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
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UniProt GroupQ68T42
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP469enterovirus D68Mutation(s): 0 
UniProt
Find proteins for Q68T42 (Human enterovirus D68)
Explore Q68T42 
Go to UniProtKB:  Q68T42
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UniProt GroupQ68T42
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Major facilitator superfamily domain-containing protein 6133Homo sapiensMutation(s): 0 
Gene Names: MFSD6MMR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZSS7 (Homo sapiens)
Explore Q6ZSS7 
Go to UniProtKB:  Q6ZSS7
PHAROS:  Q6ZSS7
GTEx:  ENSG00000151690 
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UniProt GroupQ6ZSS7
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Reference Sequence

Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F
6N/A
Glycosylation Resources
GlyTouCan: G82348BZ
GlyCosmos: G82348BZ
GlyGen: G82348BZ
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose
G
2N/A
Glycosylation Resources
GlyTouCan: G30207PZ
GlyCosmos: G30207PZ
GlyGen: G30207PZ

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-22
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references